Index – B

b (pyrosetta.rosetta.basic.sampling.orientations.Triple property) B (pyrosetta.rosetta.core.chemical.element.Elements attribute) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) b (pyrosetta.rosetta.core.scoring.packstat.PointPair property) B (pyrosetta.rosetta.protocols.comparative_modeling.features.TorsionBin attribute) (pyrosetta.rosetta.protocols.features.RamachandranHash attribute) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc property) b (pyrosetta.rosetta.protocols.md.Constraint property) (pyrosetta.rosetta.protocols.sic_dock.Vec3 property) B() (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) b1() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) b1_b2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) b1_b2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) b1_bond_angle_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_bond_angle_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_bond_angle_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2() (pyrosetta.rosetta.core.scoring.facts.FACTSRsdTypeInfo method) b2_bond_angle_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_bond_angle_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_bond_angle_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) B2I_1 (pyrosetta.rosetta.protocols.sparta.ANN property) B2I_2 (pyrosetta.rosetta.protocols.sparta.ANN property) B2I_3 (pyrosetta.rosetta.protocols.sparta.ANN property) B2L1_1 (pyrosetta.rosetta.protocols.sparta.ANN property) B2L1_2 (pyrosetta.rosetta.protocols.sparta.ANN property) B2L1_3 (pyrosetta.rosetta.protocols.sparta.ANN property) B2L2_1 (pyrosetta.rosetta.protocols.sparta.ANN property) B2L2_2 (pyrosetta.rosetta.protocols.sparta.ANN property) B2L2_3 (pyrosetta.rosetta.protocols.sparta.ANN property) B_ (pyrosetta.rosetta.core.scoring.electron_density.poseCoord property) (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) (pyrosetta.rosetta.protocols.electron_density.PoseSphericalSamplesOptions property) (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) B_0 (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc property) b_allow_independent_alignment_per_fragment (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) B_C_D_bond_angle_rad (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry property) B_C_D_E_torsion_angle_rad (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry property) B_Factor (pyrosetta.rosetta.protocols.sparta.PDB_Entry property) b_full_motif_bb_alignment (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) b_graft_only_hotspots_by_sidechain_replacement (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) b_is_full_motif_bb_alignment() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifMatch method) B_to_W (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) B_to_W_norm (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) B_to_W_norm2 (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) B_to_W_norm3 (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder property) (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinderWadj property) Ba (pyrosetta.rosetta.core.chemical.element.Elements attribute) ba (pyrosetta.rosetta.protocols.loophash.LegacyLeapIndex property) BAB_CFr (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) bab_motif() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) bab_motifs() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) BABx1 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) BABx2 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) BABx3 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) back() (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_DOF_ID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_raw_data_DisulfideFile_ResNum_core_io_raw_data_DisulfideFile_ResNum_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_aa_composition_energy_TailFunction_core_scoring_aa_composition_energy_TailFunction_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_CentroidDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_DisulfideMatchingEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_scoring_disulfides_FullatomDisulfideEnergyComponents_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_double_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_std_shared_ptr_const_core_conformation_ResidueMatcher_t method) (pyrosetta.rosetta.utility.vector1_std_pair_int_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_long_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_double_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_numeric_xyzVector_float_int_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_forge_build_Interval_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_loophash_BackboneSegment_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_protocols_sewing_data_storage_Basis_protocols_sewing_data_storage_Basis_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_list_std_shared_ptr_const_core_conformation_Residue_utility_vector1_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_std_allocator_std_shared_ptr_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_pair_unsigned_long_unsigned_long_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_set_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_const_core_pose_ResidueIndexDescription_std_shared_ptr_const_core_pose_ResidueIndexDescription_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_const_numeric_expression_parser_Expression_std_shared_ptr_protocols_pack_daemon_SurrogateVariableExpression_t method) (pyrosetta.rosetta.utility.vector1_std_pair_std_shared_ptr_core_io_silent_SilentStruct_utility_file_FileName_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) BACKBONE (pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE attribute) backbone() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) backbone_aa() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.conformation.Residue method) backbone_backbone() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) backbone_backbone_energy() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) backbone_bin (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type attribute) backbone_burial() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) backbone_database() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) backbone_exposed() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) backbone_for_moltenres_bbconf() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) backbone_for_resid_bbconf() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) backbone_mover_complex_type_namer() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover static method) backbone_only() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) backbone_only_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) backbone_sidechain() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) backbone_sidechain_energy() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) backbone_stub_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) backbone_stub_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) backbone_stub_linear_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) backbone_stub_linear_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) backbone_stub_match() (in module pyrosetta.rosetta.protocols.motifs) backbone_torsion_angle_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) BackboneDB (class in pyrosetta.rosetta.protocols.loophash) BackboneGridSampler (class in pyrosetta.rosetta.protocols.helical_bundle) BackboneGridSamplerCreator (class in pyrosetta.rosetta.protocols.helical_bundle) BackboneGridSamplerHelper (class in pyrosetta.rosetta.protocols.helical_bundle) BackboneMover (class in pyrosetta.rosetta.protocols.simple_moves) BackboneSampler (class in pyrosetta.rosetta.protocols.enzdes) BackboneSamplerCreator (class in pyrosetta.rosetta.protocols.enzdes) BackboneSegment (class in pyrosetta.rosetta.protocols.loophash) BackboneStub (class in pyrosetta.rosetta.protocols.indexed_structure_store) BackboneStubConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BackboneStubLinearConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BackboneStubRMSDComparator (class in pyrosetta.rosetta.protocols.pose_length_moves) BackboneStubVectorRMSDComparator (class in pyrosetta.rosetta.protocols.indexed_structure_store) BackboneTorsionPerturbation (class in pyrosetta.rosetta.protocols.hybridization) BackboneTorsionPerturbationCreator (class in pyrosetta.rosetta.protocols.hybridization) BackboneTorsionSampler (class in pyrosetta.rosetta.protocols.hybridization) BackboneTorsionSamplerCreator (class in pyrosetta.rosetta.protocols.hybridization) backrub_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) BACKRUB_MOVER (pyrosetta.rosetta.basic.ProfTag attribute) backrub_opt (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) backrub_protocol (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) backrub_rotation_angles() (in module pyrosetta.rosetta.protocols.backrub) backrub_rotation_constants() (in module pyrosetta.rosetta.protocols.backrub) BackrubDDMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BackrubDDMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BackrubMover (class in pyrosetta.rosetta.protocols.backrub) BackrubMoverCreator (class in pyrosetta.rosetta.protocols.backrub) BackrubProtocol (class in pyrosetta.rosetta.protocols.backrub) BackrubProtocolCreator (class in pyrosetta.rosetta.protocols.backrub) BackrubSegment (class in pyrosetta.rosetta.protocols.backrub) BackrubSidechainMover (class in pyrosetta.rosetta.protocols.backrub) BackrubSidechainMoverCreator (class in pyrosetta.rosetta.protocols.backrub) backward (pyrosetta.rosetta.protocols.carbohydrates.QuenchDirection attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ChainDirection attribute) backward_check() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) backward_jump() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) bad (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor.CompletionMessage property) bad() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.InnerMultiThreadingJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJob method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) BAD_INPUT_TAG (pyrosetta.rosetta.basic.mpi.mpi_tags attribute) BAD_LOW_PROB (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass attribute) BAD_RT6() (pyrosetta.rosetta.numeric.Py_xyzTransform_double static method) (pyrosetta.rosetta.numeric.xyzTransform_double_t static method) bad_tree() (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) BAD_XFORM() (pyrosetta.rosetta.numeric.Py_xyzTransform_double static method) (pyrosetta.rosetta.numeric.xyzTransform_double_t static method) (pyrosetta.rosetta.numeric.xyzTransform_float_t static method) badfast() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) BadInput (class in pyrosetta.rosetta.utility.excn) baho_posi() (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) BalancedKicMover (class in pyrosetta.rosetta.protocols.kinematic_closure) BalancedKicMoverCreator (class in pyrosetta.rosetta.protocols.kinematic_closure) Ball (class in pyrosetta.rosetta.core.scoring.packing) (class in pyrosetta.rosetta.numeric.geometry.hashing) ball() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) (pyrosetta.rosetta.core.scoring.packing.PoseBallsLite method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) balls() (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) BANGLE_MIN() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) BANGLE_SD() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) bare_name() (pyrosetta.rosetta.utility.file.FileName method) barea (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData property) BareMinimumPDEdge (class in pyrosetta.rosetta.core.pack.hbonds) Base (class in pyrosetta.rosetta.protocols.toolbox.py_inheritance_test) (class in pyrosetta.rosetta.utility.py) base (pyrosetta.CD property) BASE (pyrosetta.rosetta.RNAAtomType attribute) base() (pyrosetta.rosetta.protocols.dna.DNAParameters method) (pyrosetta.rosetta.utility.file.FileName method) base2_xyz() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) base5index2symbolString() (pyrosetta.rosetta.core.sequence.ABEGOManager method) base64_decode() (in module pyrosetta.rosetta.utility.io) base64_encode() (in module pyrosetta.rosetta.utility.io) base_analogue() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) base_atom_list_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) base_atoms_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) base_atr_score() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker.ProteinAtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) base_attributes() (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover static method) base_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_backbone_distance_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_backbone_rho_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_backbone_z_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) BASE_BIN_MAP (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) BASE_CENTROID (pyrosetta.rosetta.core.pose.rna.StubStubType attribute) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) base_centroids() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) base_geometry_height_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_geometry_orientation_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) BASE_NAME (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode attribute) base_name() (in module pyrosetta.rosetta.protocols.vip) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) base_native_bonus() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) base_only() (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) base_pair_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_pair_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) base_pair_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) base_pair_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) base_pair_moving() (in module pyrosetta.rosetta.core.pose.rna) base_pair_rmsd_cutoff() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) base_pair_rotation_mag() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) base_pair_score() (pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential method) base_pair_step_moving() (in module pyrosetta.rosetta.core.pose.rna) base_pair_translation_mag() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) base_pairing_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) base_pairs() (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) BASE_PARTNER (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) base_property() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) base_rep_score() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker.ProteinAtrRepChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker method) base_residue_types() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) base_stack_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stack_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stack_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) base_stack_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) base_stagger_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_state() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) base_step_energy() (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) base_step_score() (pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential method) base_stubs() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) base_type() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) base_types() (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) base_xyz (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.MyWaterHolder property) base_xyz() (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) BaseArchiveManager (class in pyrosetta.rosetta.protocols.jd2.archive) BaseBin (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body) BaseBinMapUpdater (class in pyrosetta.rosetta.protocols.stepwise.screener) BaseCacheUnit (class in pyrosetta.rosetta.core.fragment) BaseCentroidScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) BaseDisulfPairingLibrary (class in pyrosetta.rosetta.protocols.jumping) BaseDoubletOrientation (class in pyrosetta.rosetta.core.chemical.rna) BaseEdge (class in pyrosetta.rosetta.core.chemical.rna) BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t (class in pyrosetta.rosetta.core.scoring.etable) BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t (class in pyrosetta.rosetta.core.scoring.etable) BaseJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) BaseJumpSetup (class in pyrosetta.rosetta.protocols.jumping) baseline() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) baseline_checkpointing_filename() (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) baseline_val() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) basename_for_score_function() (in module pyrosetta.rosetta.core.scoring) BasePair (class in pyrosetta.rosetta.core.pose.rna) basepair() (pyrosetta.rosetta.protocols.dna.DNAParameters method) basepair_axis_stagger_scaling() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) BasePairConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BasePairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) BasePairingLibrary (class in pyrosetta.rosetta.protocols.jumping) BasePairStep (class in pyrosetta.rosetta.core.pose.rna) BasePairStepLibrary (class in pyrosetta.rosetta.core.import_pose.libraries) BasePairStepSequence (class in pyrosetta.rosetta.core.import_pose.libraries) BasePairType (class in pyrosetta.rosetta.core.import_pose.libraries) BasePartner (class in pyrosetta.rosetta.core.scoring.dna) baseres_ (pyrosetta.rosetta.protocols.loop_grower.SheetPositions property) baserotamer_data() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) BaseStack (class in pyrosetta.rosetta.core.pose.rna) basestack_axis_scaling() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) BaseStackWhichSide (class in pyrosetta.rosetta.core.chemical.rna) basestep() (pyrosetta.rosetta.protocols.dna.DNAParameters method) BaseTabooPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) BaseTypeList (class in pyrosetta.rosetta.core.pack.palette) basic_idealize() (in module pyrosetta.rosetta.protocols.idealize) basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t (class in pyrosetta.rosetta.utility.io.mpi_stream) basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t.sentry (class in pyrosetta.rosetta.utility.io.mpi_stream) basic_mpi_ostreambase_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t (class in pyrosetta.rosetta.utility.io.mpi_stream) basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t (class in pyrosetta.rosetta.utility.io.mpi_stream) basic_name() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) basic_otstream_char_std_char_traits_char_t (class in pyrosetta.rosetta.basic) basic_otstream_char_std_char_traits_char_t.sentry (class in pyrosetta.rosetta.basic) basic_selection_logic (class in pyrosetta.rosetta.core.select.residue_selector) BasicCDRClusterSet (class in pyrosetta.rosetta.protocols.antibody.clusters) BasicCmdLineInit (class in pyrosetta.rosetta.protocols.rpc) BasicDataCache (class in pyrosetta.rosetta.basic.datacache) BasicInit (class in pyrosetta.rosetta.protocols.rpc) BasicJob (class in pyrosetta.rosetta.protocols.jobdist) BasicJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) BasicRotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) BasicRotamerLibrarySpecificationCreator (class in pyrosetta.rosetta.core.chemical.rotamers) BasicSimAnnealerRepacker (class in pyrosetta.rosetta.protocols.pack_daemon) Basis (class in pyrosetta.rosetta.protocols.legacy_sewing) (class in pyrosetta.rosetta.protocols.sewing.data_storage) basis_atoms_ (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue property) basis_map() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) basis_map_from_alignment() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) basis_map_generator() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) basis_pair() (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) basis_pair_equal_to (class in pyrosetta.rosetta.protocols.legacy_sewing) basis_pair_hash (class in pyrosetta.rosetta.protocols.legacy_sewing) basis_pair_is_valid() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) basis_resnum (pyrosetta.rosetta.protocols.legacy_sewing.HashValue property) (pyrosetta.rosetta.protocols.sewing.hashing.HashValue property) basis_segment_id (pyrosetta.rosetta.protocols.sewing.hashing.HashValue property) BasisMapGenerator (class in pyrosetta.rosetta.protocols.sewing.hashing) Batch (class in pyrosetta.rosetta.protocols.jd2.archive) batch() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) batch_apply() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) batch_get_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) batch_id (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor.CompletionMessage property) batch_set_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) batches() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) BatchEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) BatchFeatures (class in pyrosetta.rosetta.protocols.features) BatchJobInputter (class in pyrosetta.rosetta.protocols.jd2) BatchNrEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) BB (pyrosetta.rosetta.core.id.TorsionType attribute) bb (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueEntry property) bb() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) BB_BB (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) bb_bb() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) BB_BINRANGE (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t property) bb_bins_from_pose() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) bb_boltz_probs() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) bb_boltz_probs_per_aa() (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) bb_bounding_sphere() (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) bb_C_index() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) bb_CA_index() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) bb_centroid() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) bb_clones() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) bb_donor_acceptor_check() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) bb_follows() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) bb_H_index() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) bb_independent_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) bb_is_independent() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) bb_movable_selector() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) bb_N_index() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) bb_O_index() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) BB_ONLY (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover.AtomSelector attribute) bb_only() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) bb_pair_score() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) BB_PH (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) BB_PO (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) BB_Pos (class in pyrosetta.rosetta.core.scoring) (class in pyrosetta.rosetta.protocols.fldsgn.topology) bb_pos() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) bb_radius() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) bb_rmsd() (in module pyrosetta.rosetta.core.scoring) bb_rmsd_including_O() (in module pyrosetta.rosetta.core.scoring) bb_stats() (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsStatistics method) bb_stdev() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) BBClaim (class in pyrosetta.rosetta.protocols.topology_broker.claims) BBClaim.ClaimRight (class in pyrosetta.rosetta.protocols.topology_broker.claims) bbconf_for_rotamer() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) bbconf_for_rotamer_on_moltenres() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) BBConRotMover (class in pyrosetta.rosetta.protocols.simple_moves) BBData (class in pyrosetta.rosetta.protocols.loophash) bbdep_angle_parameters() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) bbdep_bond_devs() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) bbdep_bond_params() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) bbdep_length_parameters() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) bbdep_nrchi_sample() (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.BBDepSemiRotamericData_2_5_t method) BBDepCartBondedParameters (class in pyrosetta.rosetta.core.scoring.methods) BBDepNRChiSample_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepNRChiSample_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepScoreInterpData_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepScoreInterpData_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepScoreInterpData_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepScoreInterpData_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepScoreInterpData_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_1_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_1_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_1_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_1_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_1_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_2_1_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_2_2_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_2_3_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_2_4_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDepSemiRotamericData_2_5_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBDihedralSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSampler2D (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSampler3D (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSamplerBase (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSamplerMover (class in pyrosetta.rosetta.protocols.simple_moves) BBDihedralSamplerMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) BBDihedralSamplerND (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBdisplay_state (pyrosetta.rosetta.protocols.viewer.GraphicsState property) BBdisplayState (class in pyrosetta.rosetta.protocols.viewer.graphics_states_param) BBDofs (class in pyrosetta.rosetta.protocols.splice) bbdofs() (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) BBExtraData (class in pyrosetta.rosetta.protocols.loophash) BBG8T3AMover (class in pyrosetta.rosetta.protocols.simple_moves) BBGaussianMover (class in pyrosetta.rosetta.protocols.simple_moves) BBGaussianMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) BBIndepCartBondedParameters (class in pyrosetta.rosetta.core.scoring.methods) BBIndNRChiSample_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) BBMatching (class in pyrosetta.rosetta.protocols.splice) bbmin (pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions property) bbnbrs() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) bbpos_is_set() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) bbs_appropriate_for_definitions() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) BBSampleType (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) bbtorsion_srfd() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) BBTorsionAndAnglesSRFD (class in pyrosetta.rosetta.core.fragment) BBTorsionSRFD (class in pyrosetta.rosetta.core.fragment) bcfl (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) bckg() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) bckg_type() (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) BCLFragmentBaseMover (class in pyrosetta.rosetta.protocols.drug_design.bcl) BCLFragmentHandler (class in pyrosetta.rosetta.core.chemical.bcl) BCLFragmentMutateMover (class in pyrosetta.rosetta.protocols.drug_design.bcl) BCLFragmentMutateMoverCreator (class in pyrosetta.rosetta.protocols.drug_design.bcl) BCLReferenceSDFilesManager (class in pyrosetta.rosetta.protocols.drug_design.bcl) BCLSampleConfsManager (class in pyrosetta.rosetta.protocols.drug_design.bcl) bCreateOutput_ (pyrosetta.rosetta.protocols.sparta.Sparta property) BDR (class in pyrosetta.rosetta.protocols.forge.components) bdx (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData property) bdy (pyrosetta.rosetta.core.scoring.packstat.LR_MP_AtomData property) Be (pyrosetta.rosetta.core.chemical.element.Elements attribute) be_lenient() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) bead_bead_interaction (pyrosetta.rosetta.core.scoring.etable.AtomPairEnergy property) become() (pyrosetta.rosetta.protocols.sewing.data_storage.LigandResidue method) (pyrosetta.rosetta.protocols.sewing.data_storage.LigandSegment static method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSegment static method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartSewingResidue method) been_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) before (pyrosetta.rosetta.protocols.denovo_design.task_operations.SurroundingSS property) before() (pyrosetta.rosetta.std.type_info method) before_chain_break_grid_index_screening (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) BEFr (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) begin (pyrosetta.rosetta.protocols.antibody.grafting.CDR_Bounds property) (pyrosetta.rosetta.protocols.features.Segment property) (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) begin() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.select.PreSelectedResidRange method) (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) (pyrosetta.rosetta.numeric.MathVector_double_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) (pyrosetta.rosetta.utility.fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_bool_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_1_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_2_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_3_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_4_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_5_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_7_t method) (pyrosetta.rosetta.utility.fixedsizearray1_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_float_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_int_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_interpolation_spline_BorderFlag_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_1_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_2_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_3_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_4_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_5_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathNTensor_double_6_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_numeric_MathVector_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_ObjexxFCL_FArray1D_double_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_protocols_match_ProbeRadius_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_std_pair_double_double_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_char_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_char_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_7_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_unsigned_short_6_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_16_16_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_2_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_32_32_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_5_5_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_64_64_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_8_8_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_1_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_2_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_3_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_4_t method) (pyrosetta.rosetta.utility.fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_5_t method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.LexicographicalIterator method) (pyrosetta.rosetta.utility.SimpleRange1 method) (pyrosetta.rosetta.utility.sql_database.session method) begin1() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) begin2() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) begin_const() (pyrosetta.rosetta.core.io.raw_data.DecoyFileData method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData method) begin_critical_section() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) begin_processing() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) begin_receptor_partner_pair() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) begin_structure() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) begin_transaction() (pyrosetta.rosetta.utility.sql_database.session method) beginBatchEdit() (pyrosetta.rosetta.RDKit.RWMol method) being_designed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) being_packed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) being_packed_ (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo property) BELOW (pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide attribute) BenchmarkBuildRotamersMover (class in pyrosetta.rosetta.protocols.testing) BenchmarkBuildRotamersMoverCreator (class in pyrosetta.rosetta.protocols.testing) bend() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) bend_angle() (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) bend_level() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) best_abs_log_norm_ratio() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) best_assignment() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) best_bbcst_residues() (in module pyrosetta.rosetta.protocols.protein_interface_design) best_by_ala_scan() (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) best_candidate_rmsds_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer property) best_cos_theta() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) best_cutpoint() (in module pyrosetta.rosetta.protocols.protein_interface_design) best_exemplar (pyrosetta.rosetta.protocols.cluster.DataPoint property) best_fit() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) best_fitness_from_current_generation() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) best_motif (pyrosetta.rosetta.core.scoring.motif.XformSummary property) best_motifhits() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) best_motifs() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) best_norm_analytic() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) best_norm_numeric() (pyrosetta.rosetta.core.optimization.NumDerivCheckData method) (pyrosetta.rosetta.core.optimization.SimpleDerivCheckResult method) best_rotamer_energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) best_rotamers() (pyrosetta.rosetta.protocols.motifs.BuildPosition method) best_score() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) bestClusMargin (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) bestClusSize (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) BestHotspotCstMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BestHotspotCstMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BestMatchesCollection (class in pyrosetta.rosetta.protocols.match.output) BestMutationsFromProbabilitiesMetric (class in pyrosetta.rosetta.core.simple_metrics.composite_metrics) BestMutationsFromProbabilitiesMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.composite_metrics) BestTotalScoreSelector (class in pyrosetta.rosetta.protocols.frag_picker) BETA (pyrosetta.rosetta.core.chemical.rna.RNA_Torsion attribute) beta (pyrosetta.rosetta.protocols.protein_interface_design.Transformation property) beta() (pyrosetta.rosetta.core.io.CrystInfo method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.dna.DNABase method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.EulerAngles method) BETA6_LINKS (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) BETA_AA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) beta_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) BETA_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) BETA_BRANCHED_SIDECHAIN (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) beta_components() (pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential method) BETA_LINKS (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) BETA_NON_METHYL (pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE attribute) BETA_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) beta_turn_distance_cutoff() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) beta_turn_length() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) beta_turn_present() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) beta_turn_type() (pyrosetta.rosetta.protocols.features.BetaTurnDetection method) BetaAlphaBetaMotif (class in pyrosetta.rosetta.protocols.fldsgn.topology) BetaAlphaBetaMotifSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) betamax (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) betamin (pyrosetta.rosetta.core.pose.rna.RNA_SuiteName property) BetaSheetArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) BetaSheetArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) BetaTurnDetection (class in pyrosetta.rosetta.protocols.features) BetaTurnDetectionFeatures (class in pyrosetta.rosetta.protocols.features) BetaTurnDetectionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) bF() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) bfac (pyrosetta.rosetta.core.scoring.packstat.SimplePDB_Atom property) bfac() (pyrosetta.rosetta.core.scoring.motif.Xfrag method) (pyrosetta.rosetta.core.scoring.packing.PoseBalls method) bfac1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) bfac2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) BFactor (class in pyrosetta.rosetta.protocols.frag_picker.scores) bfactor() (pyrosetta.rosetta.core.pose.PDBInfo method) BfactorFittingMover (class in pyrosetta.rosetta.protocols.electron_density) BfactorFittingMoverCreator (class in pyrosetta.rosetta.protocols.electron_density) BfactorMPM (class in pyrosetta.rosetta.protocols.match) BfactorMultifunc (class in pyrosetta.rosetta.protocols.electron_density) bfactors() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) BFactorSelector (class in pyrosetta.rosetta.core.select.residue_selector) BFactorSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) BFr (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) bg() (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) bgBlack (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgBlue (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgCyan (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgDefault (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgGreen (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgMagenta (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgRed (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgWhite (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) bgYellow (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) Bh (pyrosetta.rosetta.core.chemical.element.Elements attribute) Bi (pyrosetta.rosetta.core.chemical.element.Elements attribute) Bi() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) Bi_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) BI_1 (pyrosetta.rosetta.protocols.sparta.ANN property) BI_2 (pyrosetta.rosetta.protocols.sparta.ANN property) BI_3 (pyrosetta.rosetta.protocols.sparta.ANN property) bias (pyrosetta.rosetta.protocols.environment.claims.CutBiasElement property) bias_energy() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) BiasedMonteCarlo (class in pyrosetta.rosetta.protocols.canonical_sampling) BiasEnergy (class in pyrosetta.rosetta.protocols.canonical_sampling) Bicelle (class in pyrosetta.rosetta.core.conformation.membrane.membrane_geometry) BICELLE (pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION attribute) bicelle_edge_steepness() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) bicelle_inner_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) bicelle_outer_radius() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) BicubicSpline (class in pyrosetta.rosetta.numeric.interpolation.spline) bIdealLoopClosing() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) big_bin_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) bigbin() (pyrosetta.rosetta.protocols.frags.VallData method) BigBinConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BigBinConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) bin() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) bin0_of_real() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner method) bin6() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_angle() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) bin_boundaries_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) bin_boundaries_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) bin_center() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) bin_center_point() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_definition_exists() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) BIN_EQUIVALENTS (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t property) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t property) bin_exists() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) bin_exists_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) bin_exists_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) bin_extrema() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) bin_from_bond() (in module pyrosetta.rosetta.core.scoring) bin_from_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_index() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) (pyrosetta.rosetta.core.scoring.motif.XformScore method) (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_index_hasher (class in pyrosetta.rosetta.numeric.geometry.hashing) bin_matches() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) bin_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) bin_params_file_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) bin_params_loaded() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) bin_rotameric_chi() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) bin_width() (pyrosetta.rosetta.protocols.match.Bool3DGrid method) bin_widths() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) binary_function_basic_datacache_ResRotPair_basic_datacache_ResRotPair_bool_t (class in pyrosetta.rosetta.std) binary_function_std_pair_char_char_std_pair_char_char_bool_t (class in pyrosetta.rosetta.std) binary_function_unsigned_long_unsigned_long_bool_t (class in pyrosetta.rosetta.std) binary_output() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) binary_rna_output() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) BinaryExpression (class in pyrosetta.rosetta.numeric.expression_parser) BinaryFragmentStoreBackend (class in pyrosetta.rosetta.protocols.indexed_structure_store) BinarySilentStruct (class in pyrosetta.rosetta.core.io.silent) BinarySilentStructCreator (class in pyrosetta.rosetta.core.io.silent) bind() (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.statement method) bind_classmethod() (in module pyrosetta.bindings.utility) bind_data (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info property) bind_data() (pyrosetta.rosetta.basic.database.insert_statement_generator.RowDataBase method) bind_method() (in module pyrosetta.bindings.utility) bind_null() (pyrosetta.rosetta.cppdb.backend.statement method) (pyrosetta.rosetta.cppdb.statement method) bind_property() (in module pyrosetta.bindings.utility) binder_selector() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method)

binder_weight() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) BindingSiteConstraint (class in pyrosetta.rosetta.protocols.constraints_additional) BindingSiteConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) BindingStrainFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) BindingStrainFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) binname() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method) binname_index_from_string_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) binname_index_from_string_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) binner() (pyrosetta.rosetta.protocols.match.HitHasher method) bins (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode attribute) bins_per_a() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.Simulated4PDEERTraceFactory method) bins_per_A2 (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) BinSelector (class in pyrosetta.rosetta.core.select.residue_selector) BinSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) binsums_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) binsums_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) BinTransitionCalculator (class in pyrosetta.rosetta.core.scoring.bin_transitions) BinTransitionCalculatorManager (class in pyrosetta.rosetta.core.scoring.bin_transitions) BinTransitionData (class in pyrosetta.rosetta.core.scoring.bin_transitions) bio_type (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) BIOLOGICAL_UNIT (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) bisector (pyrosetta.rosetta.core.scoring.MultipoleAxisType attribute) bit_is_set() (in module pyrosetta.rosetta.core.pack.dunbrack) bit_or() (in module pyrosetta.rosetta.ObjexxFCL.bit) bit_score (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) bit_set() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome) bit_test() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome) bite() (in module pyrosetta.rosetta.ObjexxFCL.format) Bite_bool_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_char_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_double_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_float_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_int_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_long_double_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_long_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_ObjexxFCL_byte_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_ObjexxFCL_Fstring_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_ObjexxFCL_ubyte_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_short_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_signed_char_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_std_complex_double_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_std_complex_float_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_std_complex_long_double_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_std_string_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_unsigned_int_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bite_unsigned_short_t (class in pyrosetta.rosetta.ObjexxFCL.format) Bk (pyrosetta.rosetta.core.chemical.element.Elements attribute) BL1_1 (pyrosetta.rosetta.protocols.sparta.ANN property) BL1_2 (pyrosetta.rosetta.protocols.sparta.ANN property) BL1_3 (pyrosetta.rosetta.protocols.sparta.ANN property) BL2_1 (pyrosetta.rosetta.protocols.sparta.ANN property) BL2_2 (pyrosetta.rosetta.protocols.sparta.ANN property) BL2_3 (pyrosetta.rosetta.protocols.sparta.ANN property) Black (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) blank() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.core.pose.rna.RNA_SecStruct method) blank_score_terms() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) blanket_assign_state_0() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) blanket_set() (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) BlankMatrixMult() (in module pyrosetta.rosetta.numeric.model_quality) block() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_GeneralEvent_t method) block_allocation_error_message() (in module pyrosetta.rosetta.utility.graph) block_file() (pyrosetta.rosetta.protocols.jd2.DebugOut_MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.MpiFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteOut_MpiFileBuffer method) block_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) block_size() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) block_stack() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) BLOCK_STACK_ABOVE (pyrosetta.rosetta.core.chemical.VariantType attribute) block_stack_above_res() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) BLOCK_STACK_BELOW (pyrosetta.rosetta.core.chemical.VariantType attribute) block_stack_below_res() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) blocked (pyrosetta.rosetta.utility.signals.LinkUnit property) blocked() (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.Link method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.SignalHub_void_core_pose_signals_GeneralEvent_t method) blocking_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) BlockParam (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) BlockSelector (class in pyrosetta.rosetta.core.select.residue_selector) BlockSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) BlockwiseAnalysisMover (class in pyrosetta.rosetta.protocols.pose_sewing.movers) BlockwiseAnalysisMoverCreator (class in pyrosetta.rosetta.protocols.pose_sewing.movers) BlockwisePoseCompMotifMetric (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) BlockwisePoseCompMotifMetricCreator (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) BlockwiseShapeCompMetric (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) BlockwiseShapeCompMetricCreator (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) Blosum62Map (class in pyrosetta.rosetta.core.sequence) BLOSUM_62 (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) blosum_history_ (pyrosetta.rosetta.protocols.legacy_sewing.Assembly property) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly property) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly property) Blue (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) BluePrint (class in pyrosetta.rosetta.protocols.parser) blueprint (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) blueprint_cst_definition() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) BlueprintArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) BlueprintArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) BluePrintBDR (class in pyrosetta.rosetta.protocols.fldsgn) BluePrintBDRCreator (class in pyrosetta.rosetta.protocols.fldsgn) bn (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType property) bogus (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) (pyrosetta.rosetta.protocols.simple_filters.comparison_type attribute) BOGUS_ATOM_ID() (pyrosetta.rosetta.core.id.AtomID static method) BOGUS_DOF_ID() (pyrosetta.rosetta.core.id.DOF_ID static method) BOGUS_NAMED_ATOM_ID() (pyrosetta.rosetta.core.id.NamedAtomID static method) BOGUS_PARTIAL_ATOM_ID() (pyrosetta.rosetta.core.id.PartialAtomID static method) BOGUS_STUB_ID() (pyrosetta.rosetta.core.id.StubID static method) BOGUS_TORSION_ID() (pyrosetta.rosetta.core.id.TorsionID static method) BOINCJobDistributor (class in pyrosetta.rosetta.protocols.jd2) Bold (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) boltz_rank() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) boltzmann() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) boltzmann_accept_probability() (in module pyrosetta.rosetta.numeric) boltzmann_choice_post_enumerated_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) boltzmann_energy_selector (pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector.selector_type attribute) boltzmann_result() (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) BoltzmannFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) BoltzmannFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) BoltzmannRotamerMover (class in pyrosetta.rosetta.protocols.minimization_packing) BoltzmannRotamerMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) Bond (class in pyrosetta.rosetta.core.chemical) (class in pyrosetta.rosetta.RDKit) bond() (pyrosetta.rosetta.core.chemical.MutableResidueType method) bond_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) bond_angle_central_atoms_to_score() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) bond_angle_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_angle_residue_type_param_set() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) bond_geometry (pyrosetta.rosetta.core.scoring.ScoreType attribute) bond_geometry_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) bond_length() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) bond_length_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_name() (pyrosetta.rosetta.core.chemical.Bond method) bond_orientation() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) bond_ringness() (pyrosetta.rosetta.core.chemical.ResidueType method) BOND_TO_NEXT (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) BOND_TO_PREVIOUS (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) bond_type() (pyrosetta.rosetta.core.chemical.ResidueType method) bondangle() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) bondangle_index() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) BondAnglePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) bondangles_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParam method) BondAromaticity (class in pyrosetta.rosetta.core.chemical) BondConjugability (class in pyrosetta.rosetta.core.chemical) BondData (class in pyrosetta.rosetta.core.chemical.sdf) bonded_heavyatoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) bonded_hydrogens() (pyrosetta.rosetta.core.chemical.MutableResidueType method) bonded_neighbor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) bonded_neighbor_all_res() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) bonded_neighbor_types() (pyrosetta.rosetta.core.chemical.ResidueType method) bonded_neighbors() (pyrosetta.rosetta.core.chemical.MutableResidueType method) bonded_orbitals() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) BondedAtom (class in pyrosetta.rosetta.core.kinematics.tree) BondedResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) BondedResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) BondID (class in pyrosetta.rosetta.core.id) BondInfo (class in pyrosetta.rosetta.protocols.denovo_design.components) bonding_distance_threshold() (in module pyrosetta.rosetta.core.io.pose_from_sfr) BondInRing (pyrosetta.rosetta.core.chemical.BondRingness attribute) BondIsometry (class in pyrosetta.rosetta.core.chemical) BondName (class in pyrosetta.rosetta.core.chemical) BondNotInRing (pyrosetta.rosetta.core.chemical.BondRingness attribute) BondOrder (class in pyrosetta.rosetta.core.chemical) bondorders_map() (in module pyrosetta.rosetta.core.scoring) BondRingness (class in pyrosetta.rosetta.core.chemical) bondRings() (pyrosetta.rosetta.RDKit.RingInfo method) bondRingSizes() (pyrosetta.rosetta.RDKit.RingInfo method) bonds() (pyrosetta.rosetta.core.chemical.ResidueType method) bonds_from_resconn() (pyrosetta.rosetta.core.id.PartialAtomID method) bondType (pyrosetta.rosetta.core.chemical.sdf.BondData property) bonus_value() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStub method) bonus_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) Book_core_fragment_picking_old_vall_VallResidues_t (class in pyrosetta.rosetta.core.fragment.picking_old.concepts) Book_VallResidues (class in pyrosetta.rosetta.core.fragment.picking_old.concepts) Bool3DGrid (class in pyrosetta.rosetta.protocols.match) Bool3DGridKinemageWriter (class in pyrosetta.rosetta.protocols.match) bool_mask_from_resnums() (in module pyrosetta.rosetta.core.pack.task.residue_selector) bool_mask_from_task() (in module pyrosetta.rosetta.core.pack.task.residue_selector) bool_type (pyrosetta.rosetta.utility.json_spirit.Value_type attribute) boolean_operations (class in pyrosetta.rosetta.protocols.filters) (class in pyrosetta.rosetta.protocols.task_operations) BOOLEAN_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) BOOLEAN_OR (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) boolean_parameter() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) boolean_parameter_cop() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) BOOLEAN_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) BooleanExpressionCreator (class in pyrosetta.rosetta.numeric.expression_parser) BooleanExpressionScanner (class in pyrosetta.rosetta.numeric.expression_parser) BooleanOption (class in pyrosetta.rosetta.utility.options) BooleanOptionKey (class in pyrosetta.rosetta.utility.options) BooleanValuedParameter (class in pyrosetta.rosetta.core.conformation.parametric) BooleanVectorOption (class in pyrosetta.rosetta.utility.options) BooleanVectorOptionKey (class in pyrosetta.rosetta.utility.options) bools_from_sizes() (in module pyrosetta.rosetta.protocols.motifs) boost_closure_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) boost_fa_atr (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) bootstrapCATrace() (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) BorderFlag (class in pyrosetta.rosetta.numeric.interpolation.spline) born_radius() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) both_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) BOTH_SC_AND_BB (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph.Subsitution attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph.Subsitution attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph.Subsitution attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph attribute) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph.Subsitution attribute) bottom() (pyrosetta.rosetta.protocols.dna.DnaPosition method) bound() (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) Bound_bool_t (class in pyrosetta.rosetta.utility) Bound_double_t (class in pyrosetta.rosetta.utility) Bound_int_t (class in pyrosetta.rosetta.utility) Bound_std_string_t (class in pyrosetta.rosetta.utility) bound_struct() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) Bound_utility_file_FileName_t (class in pyrosetta.rosetta.utility) Bound_utility_file_PathName_t (class in pyrosetta.rosetta.utility) bound_width() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) boundaries() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) boundary_left() (pyrosetta.rosetta.core.kinematics.FoldTree method) boundary_neighs() (pyrosetta.rosetta.core.energy_methods.FAElecContextData method) boundary_right() (pyrosetta.rosetta.core.kinematics.FoldTree method) bounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) bounded_loops_from_alignment() (in module pyrosetta.rosetta.protocols.comparative_modeling) bounded_protocol() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) bounded_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) BoundedCollector_CompareTotalScore (class in pyrosetta.rosetta.protocols.frag_picker) BoundedCollector_protocols_frag_picker_CompareTotalScore_t (class in pyrosetta.rosetta.protocols.frag_picker) BoundFunc (class in pyrosetta.rosetta.core.scoring.constraints) bounding_box() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) (pyrosetta.rosetta.protocols.match.downstream.ActiveSiteGrid method) bounding_radius_for_rotamers() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) bounding_volume_from_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) BoundingBox_numeric_xyzVector_double_t (class in pyrosetta.rosetta.numeric.geometry) bounds() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) (pyrosetta.rosetta.numeric.kdtree.KDTree method) box_size (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info property) boxes_per_dimension (pyrosetta.rosetta.protocols.sewing.hashing.HasherSettings property) bp_motifhits() (pyrosetta.rosetta.protocols.motifs.MotifSearch method) bp_res() (pyrosetta.rosetta.protocols.recces.params.RECCES_Parameters method) bp_rotamers() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) BPC_atoms_per_residue (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_delta_omega0 (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_delta_omega1 (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_delta_omega1_peratom (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_delta_t (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_delta_z1_peratom (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_end_of_list (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_epsilon (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_invert_helix (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_last_parameter_to_be_sampled (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_omega0 (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_omega1 (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_Parameters (class in pyrosetta.rosetta.protocols.helical_bundle) BPC_r0 (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_r1_peratom (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_repeating_unit_offset (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_residues_per_repeat (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_set_bondangles (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_set_bondlengths (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_set_dihedrals (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_unknown_parameter (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_z0_offset (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_z1 (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) BPC_z1_offset (pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters attribute) bpdefs2map() (in module pyrosetta.rosetta.protocols.motifs) bps_moves() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) bQuickTest() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) Br (pyrosetta.rosetta.core.chemical.element.Elements attribute) br (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType property) BR() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) BR_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) BRANCH (pyrosetta.rosetta.core.id.TorsionType attribute) branch_conn (pyrosetta.rosetta.core.scoring.ScoreType attribute) branch_connect_atom_names() (pyrosetta.rosetta.core.chemical.ResidueType method) branch_connect_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) branch_length() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) BRANCH_POINT (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) branch_point() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) branch_variant_type_from_atom_name() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) branch_variant_type_from_position() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) BranchAngleOptimizer (class in pyrosetta.rosetta.protocols.branch_angle) BranchCoef1 (class in pyrosetta.rosetta.protocols.branch_angle) BranchCoef2 (class in pyrosetta.rosetta.protocols.branch_angle) BranchEnergy (class in pyrosetta.rosetta.core.energy_methods) BranchEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) branching_atomid1() (in module pyrosetta.rosetta.protocols.branch_angle) branching_atomids2() (in module pyrosetta.rosetta.protocols.branch_angle) branchopt() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) BranchParam1 (class in pyrosetta.rosetta.protocols.branch_angle) BranchParam2 (class in pyrosetta.rosetta.protocols.branch_angle) break_all_disulfides() (in module pyrosetta.rosetta.core.conformation) break_any_disulfide() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) break_disulfide() (in module pyrosetta.rosetta.core.conformation) break_disulfide_bonds() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) break_side() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) break_side_ramp() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) BRENT() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) brent_abs_tolerance() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) BrentLineMinimization (class in pyrosetta.rosetta.core.optimization) brf_always_false (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) brf_always_true (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) brf_filter_by_energy (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) brf_undefined (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour attribute) Bridge (class in pyrosetta.rosetta.protocols.forge.build) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstructionType attribute) bridge_objects() (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) bridge_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) BridgeChainsCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) BridgeChainsMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) BridgeChainsMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) bridgeObjects() (in module pyrosetta.rosetta.numeric.kinematic_closure) bridgeObjects_nonredundant() (in module pyrosetta.rosetta.numeric.kinematic_closure) broker() (pyrosetta.rosetta.protocols.environment.Environment method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) broker_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) Broker_main() (in module pyrosetta.rosetta.protocols.abinitio) broking_finished() (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) brute_move_large() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) brute_move_small() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) brute_move_small_top25() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) BruteFunGroupTK (class in pyrosetta.rosetta.protocols.kinmatch) BSAF_all_atoms (pyrosetta.rosetta.protocols.simple_filters.BSAF_mode attribute) BSAF_end_of_list (pyrosetta.rosetta.protocols.simple_filters.BSAF_mode attribute) BSAF_hydrophobic_atoms (pyrosetta.rosetta.protocols.simple_filters.BSAF_mode attribute) BSAF_mode (class in pyrosetta.rosetta.protocols.simple_filters) BSAF_polar_atoms (pyrosetta.rosetta.protocols.simple_filters.BSAF_mode attribute) bseq_posi() (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) bSkipStage1_ (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio property) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints property) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper property) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio property) bSkipStage2_ (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio property) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints property) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper property) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio property) bSkipStage3_ (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio property) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints property) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper property) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio property) bSkipStage4_ (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio property) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints property) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper property) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio property) bSkipStage5_ (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio property) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints property) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper property) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio property) BT_ALPHA_AA (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_AROMATIC (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_BETA_AA (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_CHARGED (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_CYCLIC (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_D_AA (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_DISULFIDE_BONDED (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_END_OF_LIST (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_L_AA (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_METALBINDING (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_POLAR (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_PROPERTIES (class in pyrosetta.rosetta.core.scoring.bin_transitions) BT_PROTEIN (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_SIDECHAIN_THIOL (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) BT_UNKNOWN_PROPERTY (pyrosetta.rosetta.core.scoring.bin_transitions.BT_PROPERTIES attribute) btcr() (pyrosetta.rosetta.protocols.tcr.TCRseqInfo method) btmplt() (pyrosetta.rosetta.protocols.tcr.TCRmodel method) BTSB_D_AA (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) BTSB_D_PRO (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) BTSB_END_OF_LIST (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) BTSB_GLY (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) BTSB_L_AA (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) BTSB_L_PRO (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) BTSB_NONE (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) BTSB_SUBBIN_TYPE (class in pyrosetta.rosetta.core.scoring.bin_transitions) BTSB_UNKNOWN (pyrosetta.rosetta.core.scoring.bin_transitions.BTSB_SUBBIN_TYPE attribute) bucket() (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) bucket_count() (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) bucket_size() (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) buckle() (pyrosetta.rosetta.protocols.dna.DNABasepair method) buf() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.PyTracer method) buf_to_address() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer method) BUFFER (class in pyrosetta.rosetta.core.io.serialization) buffer() (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) buffer_limit() (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) buffer_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) buffer_size() (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_conformation_signals_LengthEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_conformation_signals_XYZEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_pose_signals_ConformationEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_pose_signals_DestructionEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_pose_signals_EnergyEvent_t (class in pyrosetta.rosetta.utility.signals) BufferedSignalHub_void_core_pose_signals_GeneralEvent_t (class in pyrosetta.rosetta.utility.signals) buffering() (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_chemical_RestypeDestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_ConnectionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_IdentityEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_LengthEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_conformation_signals_XYZEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_ConformationEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_DestructionEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_EnergyEvent_t method) (pyrosetta.rosetta.utility.signals.BufferedSignalHub_void_core_pose_signals_GeneralEvent_t method) (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) buffering_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) build() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) (pyrosetta.rosetta.core.import_pose.FullModelPoseBuilder method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamBuilder method) (pyrosetta.rosetta.protocols.match.downstream.LigandConformerBuilder method) (pyrosetta.rosetta.protocols.match.downstream.RigidLigandBuilder method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamBuilder method) build_aa_matrix() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) build_anchorless_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_and_discard_first_round_hits_at_all_positions() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) build_and_score_disulfide() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) build_atom_ideal() (pyrosetta.rosetta.core.conformation.Residue method) build_backbone_rotamer_clouds() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) build_base_rotamers() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) build_centroid_loop() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) build_chemical_edge() (in module pyrosetta.rosetta.core.conformation) build_combined_pose_with_zinc_overlay() (pyrosetta.rosetta.protocols.metal_interface.MatchGrafter method) build_constraints() (pyrosetta.rosetta.protocols.abinitio.AlternativePairings method) (pyrosetta.rosetta.protocols.abinitio.StrandConstraints method) build_cst_conformer_jumps() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) build_dependent_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) build_dependent_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_dna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_fake_xyz() (pyrosetta.rosetta.core.kinematics.Stub method) build_fold_tree() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) build_frame_and_rotate() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) build_from_three_coords() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) build_full_model() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) build_fullatom_loop() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) build_helix() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) build_hits_at_all_positions() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) build_ideal_segment() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) build_independent_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_init_pose() (pyrosetta.rosetta.core.import_pose.RNA_HelixAssembler method) build_inverted_rotamers() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) build_jump_edge() (in module pyrosetta.rosetta.core.conformation) build_lattice_of_virtuals() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) build_layer_of_virtuals() (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) build_lkboverlap_rotamer_clouds() (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) build_loops() (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) build_orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) build_point() (pyrosetta.rosetta.protocols.match.Matcher method) build_polymer_edge() (in module pyrosetta.rosetta.core.conformation) build_pose() (in module pyrosetta.rosetta.core.import_pose) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) build_pose_as_is() (in module pyrosetta.rosetta.core.import_pose) build_pose_as_is2() (in module pyrosetta.rosetta.core.import_pose) build_pose_from_pdb_as_is() (in module pyrosetta.rosetta.core.io.pdb) build_positionOPs() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) build_pwat_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) build_random_dna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_receptor_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) build_residue_tree() (in module pyrosetta.rosetta.core.conformation) build_rna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) build_rot_matrix_for_pose() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) build_rotamer() (pyrosetta.rosetta.protocols.motifs.MotifHit method) build_rotamer_list() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) build_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) build_rotamers_from_rotamer_bins() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_rotamers_lite() (in module pyrosetta.rosetta.protocols.motifs) build_rotated_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_round1_hits_twice() (pyrosetta.rosetta.protocols.match.MatcherTask method) build_sc_only_rotamer() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) build_set() (pyrosetta.rosetta.protocols.match.upstream.ProteinUpstreamBuilder method) build_sidechain_rotamers() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) build_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) build_structures() (pyrosetta.rosetta.protocols.loophash.LoopHashSampler method) build_temperature_list() (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) build_tree() (in module pyrosetta.rosetta.core.conformation) build_waters() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) build_xyz() (pyrosetta.rosetta.core.chemical.MutableICoorRecord static method) buildable() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) buildAdjacentLists() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) BuildAlaPose (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BuildAlaPoseCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BuildDeNovoBackboneMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) BuildDeNovoBackboneMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) buildDisulfide (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) builders() (pyrosetta.rosetta.core.scoring.lkball.WaterBuilderForRestype method) BuildingBlockInterfaceOperation (class in pyrosetta.rosetta.protocols.matdes) BuildingBlockInterfaceOperationCreator (class in pyrosetta.rosetta.protocols.matdes) BuildInstruction (class in pyrosetta.rosetta.protocols.forge.build) BuildManager (class in pyrosetta.rosetta.protocols.forge.build) BuildPhases (class in pyrosetta.rosetta.protocols.denovo_design.components) BuildPosition (class in pyrosetta.rosetta.protocols.motifs) BuildPosition_from_Size() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) BuildSet (class in pyrosetta.rosetta.protocols.match.upstream) buildsturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) buildtype() (pyrosetta.rosetta.protocols.parser.BluePrint method) built_atom() (pyrosetta.rosetta.core.chemical.AtomICoor method) BULGE (pyrosetta.rosetta.core.chemical.VariantType attribute) BULGE_APPLIER (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) bulge_at_chain_closure_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) bulge_keyname() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect static method) bulge_res (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) bulge_res_base_state (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) bulge_res_pucker_state (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) bulge_suite (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) BulgeApplier (class in pyrosetta.rosetta.protocols.stepwise.screener) BulgeApplyMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge) BULGED_G (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) BulgeUnApplyMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge) bump_check() (in module pyrosetta.rosetta.core.pack.rotamer_set) (in module pyrosetta.rosetta.protocols.nmr) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSet method) bump_check_backbone() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) bump_check_full() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) BUMP_ENERGY (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel attribute) (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel.CONFORMER_FILTER attribute) bump_energy_backbone() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) bump_energy_full() (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) bump_filter() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) bump_grid() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) bump_grid_to_enclose_pose() (in module pyrosetta.rosetta.protocols.match) bump_grid_to_enclose_residue() (in module pyrosetta.rosetta.protocols.match) bump_grid_to_enclose_residue_backbone() (in module pyrosetta.rosetta.protocols.match) bump_parameter() (pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW method) bump_parameter_rnp() (pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW method) BumpGrid (class in pyrosetta.rosetta.protocols.match) BumpSelector (class in pyrosetta.rosetta.core.pack.rotamer_set) BumpSelectorDecision (class in pyrosetta.rosetta.core.pack.rotamer_set) bundle_calculator() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters method) bundle_symmetry() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) bundle_symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) BundleGridSampler (class in pyrosetta.rosetta.protocols.helical_bundle) BundleGridSamplerCreator (class in pyrosetta.rosetta.protocols.helical_bundle) BundleGridSamplerHelper (class in pyrosetta.rosetta.protocols.helical_bundle) BundleParameters (class in pyrosetta.rosetta.protocols.helical_bundle.parameters) BundleParametersSet (class in pyrosetta.rosetta.protocols.helical_bundle.parameters) bundleparametersset_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) BundleParametrizationCalculator (class in pyrosetta.rosetta.protocols.helical_bundle) BundleReporterFilter (class in pyrosetta.rosetta.protocols.helical_bundle) BundleReporterFilterBehaviour (class in pyrosetta.rosetta.protocols.helical_bundle) BundleReporterFilterCreator (class in pyrosetta.rosetta.protocols.helical_bundle) burial (pyrosetta.rosetta.core.scoring.ScoreType attribute) burial() (pyrosetta.rosetta.core.scoring.motif.Xfrag method) burial_sigmoid() (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) burial_threshold() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphOptions method) burial_v2 (pyrosetta.rosetta.core.scoring.ScoreType attribute) Burial_v2Energy (class in pyrosetta.rosetta.core.energy_methods) Burial_v2EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) BurialEnergy (class in pyrosetta.rosetta.core.energy_methods) BurialEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) buried (pyrosetta.rosetta.core.scoring.sc._DOT property) (pyrosetta.rosetta.core.scoring.sc.Atom property) buried_area (pyrosetta.rosetta.core.scoring.packstat.AreaAccumulator property) BURIED_UNSAT_HBOND_GRAPH (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) buried_unsatisfied_penalty (pyrosetta.rosetta.core.scoring.ScoreType attribute) buried_unsatisfied_penalty_burial_threshold() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_angle_exponent() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_angle_shift_factor() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_dist_exponent() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_cone_dist_midpoint() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) buried_unsatisfied_penalty_hbond_energy_threshold() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) BuriedPolarScore (class in pyrosetta.rosetta.protocols.sic_dock) BuriedSurfaceAreaFilter (class in pyrosetta.rosetta.protocols.simple_filters) BuriedSurfaceAreaFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) BuriedUnsatHbondFilter (class in pyrosetta.rosetta.protocols.simple_filters) BuriedUnsatHbondFilter2 (class in pyrosetta.rosetta.protocols.buns) BuriedUnsatHbondFilter2Creator (class in pyrosetta.rosetta.protocols.buns) BuriedUnsatHbondFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) BuriedUnsatisfiedPolarsCalculator (class in pyrosetta.rosetta.protocols.simple_pose_metric_calculators) BuriedUnsatisfiedPolarsCalculator2 (class in pyrosetta.rosetta.protocols.buns) BuriedUnsatPenalty (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty) BuriedUnsatPenaltyCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty) BuriedUnsatPenaltyEdge (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyEdgeData (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraph (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphContainer (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphHbond (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyGraphOptions (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyNode (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) BuriedUnsatPenaltyNodeData (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph) burunsat_atoms() (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) BUTYRYL_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) bx_init() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) by_aln() (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) byte (class in pyrosetta.rosetta.ObjexxFCL) byte_for_element() (pyrosetta.rosetta.utility.DenseBoolMap_5_0_t static method) bytes() (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringstream method)